From e0fa0145e3a8fd664f14b39ed806c473a18ee07f Mon Sep 17 00:00:00 2001 From: Desmond Orton Date: Fri, 28 May 2021 09:07:52 -0600 Subject: freebayes: add v1.3.5, move to MesonPackage (#23772) --- .../repos/builtin/packages/freebayes/package.py | 30 ++++++++++++++++++++-- 1 file changed, 28 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/freebayes/package.py b/var/spack/repos/builtin/packages/freebayes/package.py index 0f35c5609e..471554e32f 100644 --- a/var/spack/repos/builtin/packages/freebayes/package.py +++ b/var/spack/repos/builtin/packages/freebayes/package.py @@ -6,27 +6,53 @@ from spack import * -class Freebayes(MakefilePackage): +class Freebayes(MesonPackage): """Bayesian haplotype-based genetic polymorphism discovery and genotyping.""" homepage = "https://github.com/ekg/freebayes" + url = "https://github.com/freebayes/freebayes/releases/download/v1.3.5/freebayes-1.3.5-src.tar.gz" git = "https://github.com/ekg/freebayes.git" + version('1.3.5', sha256='7e2635690e916ed85cec36b3263e6e5357413a4f2bf3035362d9749335e8a696') version('1.1.0', commit='39e5e4bcb801556141f2da36aba1df5c5c60701f', - submodules=True) + submodules=True, deprecated=True) depends_on('cmake', type='build') depends_on('zlib') + # Deps for @1.3.5 and beyond + depends_on('ninja', type='build', when='@1.3.5:') + depends_on('htslib', when='@1.3.5:') + depends_on('zlib', when='@1.3.5:') + depends_on('xz', when='@1.3.5:') + depends_on('parallel', when='@1.3.5:') + depends_on('vcftools', when='@1.3.5:') + depends_on('bc', when='@1.3.5:') + depends_on('samtools', when='@1.3.5:') + parallel = False + @when('@:1.1.0') def edit(self, spec, prefix): makefile = FileFilter('Makefile') b = prefix.bin makefile.filter('cp bin/freebayes bin/bamleftalign /usr/local/bin/', 'cp bin/freebayes bin/bamleftalign {0}'.format(b)) + @when('@:1.1.0') @run_before('install') def make_prefix_dot_bin(self): mkdir(prefix.bin) + + @when('@:1.1.0') + def meson(self, spec, prefix): + pass + + @when('@:1.1.0') + def build(self, spec, prefix): + make() + + @when('@:1.1.0') + def install(self, spec, prefix): + make('install') -- cgit v1.2.3-60-g2f50